Pathway Analysis for Cox regression Glmnet (lambda.min)
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
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## multiMiR database URL has been set to the
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## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
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## Please cite:
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## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
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## select## library(stringr)
library(ggplot2)The results here are deprecated in favor of lambda.1se Cox Glmnet.
0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.glmnet.cox = readRDS("data/sel_features/results_glmnet_cox_coef.rds")
sel.features = results.glmnet.cox
sel.features## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$dev
## hsa-mir-101-2 hsa-mir-125a hsa-mir-1277 hsa-mir-1307 hsa-mir-130b
## -0.350155993 -0.214528093 -0.992011646 0.772882470 0.102110997
## hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c hsa-mir-3199-1
## 0.111474373 0.306494391 0.409242447 -0.164814191 -0.188845820
## hsa-mir-320c-2 hsa-mir-375 hsa-mir-3912 hsa-mir-3923 hsa-mir-513a-2
## -0.443119925 0.066404104 -0.008097655 0.190177197 -0.024029228
## hsa-mir-513b hsa-mir-605 hsa-mir-625 hsa-mir-659 hsa-mir-664
## -0.020939139 -0.120147454 -0.098469616 -0.182484891 -0.799992602
## hsa-mir-7-1 hsa-mir-874 MRE11A.R2Gn AKT1.R2Gn RAD51.R2Gn
## 1.148233824 -0.137903989 0.389314476 -0.159434639 0.845634933
## MAPK9.R2Gn MAPK3.R2Gn STMN1.R2Gn CHEK1.R2Gn ACACA.R2Gn
## -0.188024741 -0.742060120 0.008038958 0.767719561 0.174201855
## WWTR1.R2Gn CDK1.R2Gn EEF2K.R2Gn BCL2L1.R2Gn TYMS.R2Gn
## 0.136573360 0.161836438 -0.497987521 -0.069660519 0.302743158
## FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn RET.R2Gn TFRC.RPPA
## 0.577031225 -1.626099874 -0.090385350 0.447771957 0.120146812
## CLDN7.g LCN2.g PTCH1.g ANXA1.g SYK.g
## -0.176602768 0.017903924 0.017683893 0.338981167 0.017503331
##
## $fold3$elasticnet_0.5$c
## hsa-mir-101-2 hsa-mir-106b hsa-mir-1248 hsa-mir-125a hsa-mir-1274b
## -1.1694665475 0.9939393131 0.0672855648 -0.0880316837 0.0413862603
## hsa-mir-1277 hsa-mir-1307 hsa-mir-130b hsa-mir-141 hsa-mir-199a-1
## -2.1470224865 2.4683436568 0.3610700379 0.0553130529 0.4249486572
## hsa-mir-199a-2 hsa-mir-199b hsa-mir-205 hsa-mir-214 hsa-mir-29b-2
## 0.6303162842 0.7774098133 -0.2308378206 0.2173213142 -0.0496921973
## hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-330 hsa-mir-34a
## -0.5710787182 -0.3552181895 -0.8289791394 0.6217391706 -0.4020065803
## hsa-mir-3682 hsa-mir-375 hsa-mir-3912 hsa-mir-3923 hsa-mir-3926-2
## 0.3216882596 0.5288068992 -0.8446616535 0.4345049389 -0.3558452034
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-585 hsa-mir-605 hsa-mir-618
## -0.1193808139 -0.1813210601 -0.0562017121 -0.1091441112 0.0143143416
## hsa-mir-625 hsa-mir-659 hsa-mir-664 hsa-mir-670 hsa-mir-7-1
## -0.3807221774 -0.4441593672 -1.1888078114 -0.0222466593 2.5098621174
## hsa-mir-874 hsa-mir-942 hsa-mir-98 PRKCD.R2Gn MRE11A.R2Gn
## -0.7490715485 0.7935448724 -0.0186144163 -0.1722509236 0.9919023793
## BCL2L11.R2Gn AKT1.R2Gn RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn
## -1.1441582713 -0.2532545544 1.9596943782 -0.7722498402 -1.5255831798
## TSC2.R2Gn ANLN.R2Gn STMN1.R2Gn CHEK1.R2Gn ACACA.R2Gn
## -0.9241345286 0.1201372547 0.2872013887 0.8235879048 0.6425941521
## WWTR1.R2Gn CDK1.R2Gn EEF2K.R2Gn BCL2L1.R2Gn TYMS.R2Gn
## 0.6090214863 0.5051537025 -1.0936388403 -0.3779508474 0.9823122125
## PRKAA1.R2Gn FOXM1.R2Gn XIAP.R2Gn TFRC.R2Gn PREX1.R2Gn
## -0.0737130824 0.9429754576 -3.0339719950 0.0280523460 -0.2536857447
## RET.R2Gn INPP4B.RPPA TFRC.RPPA MRE11A.M PRDX1.M
## 1.6495446315 -0.0020651078 0.2151841797 0.6657256474 0.6609214928
## CASP8.M CLDN7.g YWHAE.g LCN2.g PRKCA.g
## 0.6565872959 -0.7049847863 -0.0001312615 0.4015385931 -0.0043660472
## PTCH1.g ANXA1.g SYK.g
## 0.3456107175 0.6449071241 0.3445385423
##
##
## $fold3$lasso
## $fold3$lasso$dev
## hsa-mir-1277 hsa-mir-199b hsa-mir-320c-2 hsa-mir-3923 hsa-mir-605
## -0.4394996 0.3837893 -0.5630734 0.2036978 -0.2603078
## hsa-mir-664 hsa-mir-7-1 MAPK3.R2Gn CHEK1.R2Gn FOXM1.R2Gn
## -0.5998023 1.4806307 -0.7712527 0.1470129 1.2302967
## XIAP.R2Gn PREX1.R2Gn RET.R2Gn TFRC.RPPA ANXA1.g
## -3.2083424 -0.1273675 0.2230730 0.1582401 0.3253384
##
## $fold3$lasso$c
## hsa-mir-199b hsa-mir-320c-2 hsa-mir-3923 hsa-mir-605 hsa-mir-664
## 0.05513951 -0.20961965 0.11298397 -0.02772348 -1.55408650
## hsa-mir-7-1 MAPK3.R2Gn FOXM1.R2Gn XIAP.R2Gn TFRC.RPPA
## 0.43950110 -0.61489862 1.18618843 -1.63439254 0.08341764
## ANXA1.g
## 0.01920368
##
##
##
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$dev
## hsa-mir-101-2 hsa-mir-125a hsa-mir-1277 hsa-mir-1307 hsa-mir-130b
## -0.2487331002 -0.2138861754 -0.7237625743 0.5319734262 0.0962757577
## hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c hsa-mir-3199-1
## 0.0305729960 0.2274006887 0.3316056764 -0.1219358392 -0.1370852349
## hsa-mir-320c-2 hsa-mir-3923 hsa-mir-513a-2 hsa-mir-513b hsa-mir-605
## -0.3568352118 0.1713901420 -0.0009106425 -0.0280204290 -0.1043171173
## hsa-mir-659 hsa-mir-664 hsa-mir-7-1 hsa-mir-874 MRE11A.R2Gn
## -0.0213122856 -0.8787615701 0.8237097189 -0.0457758136 0.2093189696
## AKT1.R2Gn RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn STMN1.R2Gn
## -0.0821184996 0.6485341074 -0.1381725768 -0.6903401762 0.0094342060
## CHEK1.R2Gn ACACA.R2Gn WWTR1.R2Gn CDK1.R2Gn EEF2K.R2Gn
## 0.7224003758 0.0930371590 0.0280686906 0.1643475351 -0.4101522402
## BCL2L1.R2Gn TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn
## -0.0111451156 0.1984583172 0.5764641758 -1.4422087427 -0.0990588693
## RET.R2Gn TFRC.RPPA CLDN7.g ANXA1.g
## 0.2341015550 0.0989335121 -0.0902252283 0.2727080779
##
## $fold5$elasticnet_0.5$c
## hsa-mir-101-1 hsa-mir-101-2 hsa-mir-106b hsa-mir-1248 hsa-mir-125a
## -0.201308360 -1.773219117 1.976720264 0.086115803 -0.261421179
## hsa-mir-1274b hsa-mir-1277 hsa-mir-1307 hsa-mir-130b hsa-mir-135b
## 0.202062481 -2.692688527 3.354246674 0.758584236 0.028233851
## hsa-mir-141 hsa-mir-182 hsa-mir-183 hsa-mir-199a-1 hsa-mir-199a-2
## 0.231196842 0.157599528 0.080580175 0.613351302 0.821912752
## hsa-mir-199b hsa-mir-200c hsa-mir-205 hsa-mir-214 hsa-mir-218-2
## 0.994060971 0.021174050 -0.338170725 0.482140928 0.233180872
## hsa-mir-24-2 hsa-mir-29b-1 hsa-mir-29b-2 hsa-mir-29c hsa-mir-3199-1
## 0.283680849 -0.002391981 -0.289665106 -0.895073393 -0.439936080
## hsa-mir-320c-2 hsa-mir-330 hsa-mir-34a hsa-mir-34b hsa-mir-3651
## -1.044015317 0.826943948 -0.589169348 -0.110954508 0.132388904
## hsa-mir-3682 hsa-mir-375 hsa-mir-378c hsa-mir-3912 hsa-mir-3923
## 0.651063342 0.623843699 -0.037982216 -1.343478336 0.567109871
## hsa-mir-3926-2 hsa-mir-506 hsa-mir-513a-2 hsa-mir-513b hsa-mir-514-1
## -0.518159096 -0.096647517 -0.209765225 -0.323526454 -0.118733228
## hsa-mir-514-2 hsa-mir-514-3 hsa-mir-585 hsa-mir-605 hsa-mir-618
## -0.047805602 -0.103089491 -0.155063543 -0.084879510 0.251193194
## hsa-mir-625 hsa-mir-639 hsa-mir-659 hsa-mir-664 hsa-mir-670
## -0.570359326 0.066322151 -0.421888900 -1.565739054 -0.252330829
## hsa-mir-675 hsa-mir-7-1 hsa-mir-874 hsa-mir-935 hsa-mir-942
## 0.081285594 3.049883209 -1.053395300 0.030234096 1.448856059
## hsa-mir-98 PRKCD.R2Gn MRE11A.R2Gn BCL2L11.R2Gn AKT1.R2Gn
## -0.430520066 -0.509651360 1.565059709 -2.432203359 -0.274855383
## RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn TSC2.R2Gn YBX1.R2Gn
## 2.806088205 -1.181946610 -1.955540830 -1.670483259 0.171588972
## ANLN.R2Gn STMN1.R2Gn CHEK1.R2Gn ACACA.R2Gn WWTR1.R2Gn
## 0.334199263 0.484933216 1.174045018 1.013673285 1.020686914
## CDK1.R2Gn EEF2K.R2Gn E2F1.R2Gn BCL2L1.R2Gn TYMS.R2Gn
## 0.753225907 -1.429715064 0.125645209 -0.485993782 1.483321848
## CCNB1.R2Gn PRKAA1.R2Gn FOXM1.R2Gn XIAP.R2Gn EZH2.R2Gn
## 0.141516835 -0.253035531 1.294900486 -3.909023944 0.038030836
## TFRC.R2Gn PREX1.R2Gn RET.R2Gn RBM15.RPPA FASN.RPPA
## 0.090703812 -0.362755183 2.247752934 0.001166909 0.007560847
## INPP4B.RPPA PRDX1.RPPA XBP1.RPPA MYH11.RPPA TFRC.RPPA
## -0.086372376 -0.023970279 -0.003008107 -0.032501540 0.275985560
## MRE11A.M PRDX1.M CASP8.M RPS6KA1.g CLDN7.g
## 0.910710965 0.900001325 0.892586976 -0.008094269 -0.963983420
## YWHAE.g TSC1.g LCN2.g YBX1.g PRKCA.g
## -0.253692611 0.016487783 0.685000188 -0.015758124 -0.206429629
## TTF1.g STMN1.g LCK.g PTCH1.g NRG1.g
## 0.015023530 -0.005567201 -0.014720701 0.563989120 -0.013630544
## ANXA1.g ARID1A.g CASP9.g SYK.g
## 0.789714277 -0.005287740 -0.049204012 0.561479894
##
##
## $fold5$lasso
## $fold5$lasso$dev
## hsa-mir-1277 hsa-mir-199b hsa-mir-320c-2 hsa-mir-3923 hsa-mir-605
## -0.67773818 0.62816836 -0.83120225 0.30885307 -0.40239153
## hsa-mir-7-1 MAPK3.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn
## 2.30548432 -0.93163045 1.27399975 -4.55339637 -0.31389159
## RET.R2Gn TFRC.RPPA CLDN7.g ANXA1.g
## 0.92385933 0.23700126 -0.07317507 0.47557184
##
## $fold5$lasso$c
## hsa-mir-1277 hsa-mir-1307 hsa-mir-199b hsa-mir-206 hsa-mir-3199-1
## -8.599721014 2.381186070 0.757142663 0.578828208 -0.019996140
## hsa-mir-320c-2 hsa-mir-34b hsa-mir-3912 hsa-mir-3923 hsa-mir-605
## -3.506592441 -0.005931603 -1.778975918 1.717924552 -0.292410032
## hsa-mir-659 hsa-mir-7-1 PRKCD.R2Gn TGM2.R2Gn EEF2K.R2Gn
## -0.687612334 10.532592779 -0.964084574 -0.095915019 -0.002119239
## TYMS.R2Gn XIAP.R2Gn PREX1.R2Gn RET.R2Gn TFRC.RPPA
## 5.861599651 -14.760541137 -1.054684473 4.288179571 0.977957115
## CLDN7.g LCN2.g ANXA1.g
## -0.980562035 0.007399925 1.346039542
##
##
##
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$dev
## hsa-mir-101-2 hsa-mir-1248 hsa-mir-125a hsa-mir-1277 hsa-mir-1307
## -0.380733378 0.005417786 -0.212753463 -1.097413125 0.890227464
## hsa-mir-130b hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c
## 0.106661442 0.147070108 0.340762226 0.444364704 -0.183946171
## hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-330 hsa-mir-34a hsa-mir-375
## -0.208247651 -0.481071547 0.022451088 -0.006020326 0.103285010
## hsa-mir-3912 hsa-mir-3923 hsa-mir-513a-2 hsa-mir-513b hsa-mir-605
## -0.043485404 0.201580727 -0.032413924 -0.023723027 -0.121922078
## hsa-mir-625 hsa-mir-659 hsa-mir-664 hsa-mir-7-1 hsa-mir-874
## -0.157904055 -0.250608682 -0.769339432 1.314703922 -0.192661457
## MRE11A.R2Gn AKT1.R2Gn RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn
## 0.459972690 -0.190817233 0.932827503 -0.221266059 -0.793580783
## STMN1.R2Gn CHEK1.R2Gn ACACA.R2Gn WWTR1.R2Gn CDK1.R2Gn
## 0.008947456 0.771942369 0.211037000 0.156130430 0.168859365
## EEF2K.R2Gn BCL2L1.R2Gn TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn
## -0.545750898 -0.099504495 0.359293058 0.584257453 -1.713000369
## PREX1.R2Gn RET.R2Gn TFRC.RPPA MRE11A.M PRDX1.M
## -0.080329221 0.551579545 0.128505126 0.020265007 0.019000912
## CASP8.M CLDN7.g LCN2.g PTCH1.g ANXA1.g
## 0.017616576 -0.209202528 0.043701084 0.032915897 0.366740940
## SYK.g
## 0.032538271
##
## $fold10$elasticnet_0.5$c
## hsa-mir-101-2 hsa-mir-1248 hsa-mir-125a hsa-mir-1277 hsa-mir-1307
## -0.3743394226 0.0014064170 -0.2098131809 -1.0615988337 0.8538411932
## hsa-mir-130b hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-29c
## 0.1008589375 0.1344075653 0.3283759475 0.4311534943 -0.1760670088
## hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-330 hsa-mir-375 hsa-mir-3912
## -0.2035108945 -0.4684815177 0.0020100454 0.0943467281 -0.0268227969
## hsa-mir-3923 hsa-mir-513a-2 hsa-mir-513b hsa-mir-605 hsa-mir-625
## 0.1971808416 -0.0314791009 -0.0226278363 -0.1228908997 -0.1445423962
## hsa-mir-659 hsa-mir-664 hsa-mir-7-1 hsa-mir-874 MRE11A.R2Gn
## -0.2325442678 -0.7735961116 1.2614344211 -0.1745783158 0.4458196946
## AKT1.R2Gn RAD51.R2Gn MAPK9.R2Gn MAPK3.R2Gn STMN1.R2Gn
## -0.1831727360 0.9051518480 -0.2079256975 -0.7665676549 0.0081459419
## CHEK1.R2Gn ACACA.R2Gn WWTR1.R2Gn CDK1.R2Gn EEF2K.R2Gn
## 0.7786765864 0.1980764980 0.1633067630 0.1654077390 -0.5257128074
## BCL2L1.R2Gn TYMS.R2Gn FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn
## -0.0869265810 0.3401955911 0.5783857162 -1.6858835763 -0.0852994606
## RET.R2Gn TFRC.RPPA MRE11A.M PRDX1.M CASP8.M
## 0.5149394140 0.1260665458 0.0036573052 0.0016799307 0.0005799475
## CLDN7.g LCN2.g PTCH1.g ANXA1.g SYK.g
## -0.2006189206 0.0346504587 0.0257076791 0.3573753984 0.0252179798
##
##
## $fold10$lasso
## $fold10$lasso$dev
## hsa-mir-1277 hsa-mir-199b hsa-mir-320c-2 hsa-mir-3923 hsa-mir-605
## -0.20697924 0.27101137 -0.45836489 0.16268941 -0.20086620
## hsa-mir-664 hsa-mir-7-1 MAPK3.R2Gn FOXM1.R2Gn XIAP.R2Gn
## -0.99585084 1.15564264 -0.71175862 1.25987310 -2.66585354
## PREX1.R2Gn TFRC.RPPA ANXA1.g
## -0.07326543 0.13317715 0.24514283
##
## $fold10$lasso$c
## hsa-mir-1248 hsa-mir-1277 hsa-mir-199b hsa-mir-3199-1 hsa-mir-320c-2
## 0.024224712 -1.278133246 0.864526911 -0.078510146 -1.174025346
## hsa-mir-3912 hsa-mir-3923 hsa-mir-605 hsa-mir-659 hsa-mir-7-1
## -0.275734483 0.410449853 -0.468817660 -0.153424440 3.402876154
## AKT1.R2Gn MAPK3.R2Gn WWTR1.R2Gn RAB11B.R2Gn TYMS.R2Gn
## -0.005319532 -0.761099817 0.007425546 -0.210285468 0.175029702
## FOXM1.R2Gn XIAP.R2Gn PREX1.R2Gn RET.R2Gn TFRC.RPPA
## 1.324306495 -5.948007671 -0.478619972 1.537704089 0.333768394
## CLDN7.g ANXA1.g
## -0.135997589 0.6401720451. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
#Mutations and gistict for glmnet only
out.M = variable.list[endsWith(variable.list, ".M")]
out.g = variable.list[endsWith(variable.list, ".g")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA,
"Mutations" = out.M,
"gistict" = out.g)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
M.genes = str_remove(multiomics.list[[4]], ".M")
g.genes = str_remove(multiomics.list[[5]], ".g")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
out = as.character(unique(out1))
out
}Some microRNAs are dropped as they do not contribute enough to convert to genes.
geneNames <- list("3F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$dev)),
"3F_0.5_C" = multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$c)),
"3F_1_DEV" = multiomics.to.GENES(names(sel.features$fold3$lasso$dev), drop.miRNA = T),
"3F_1_C" = multiomics.to.GENES(names(sel.features$fold3$lasso$c), drop.miRNA = T),
"5F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$dev), drop.miRNA = T),
"5F_0.5_C" = multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$c)),
"5F_1_DEV" = multiomics.to.GENES(names(sel.features$fold5$lasso$dev), drop.miRNA = T),
"5F_1_C" = multiomics.to.GENES(names(sel.features$fold5$lasso$c)),
"10F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$dev)),
"10F_0.5_C" = multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$c)),
"10F_1_DEV" = multiomics.to.GENES(names(sel.features$fold10$lasso$dev), drop.miRNA = T),
"10F_1_C" = multiomics.to.GENES(names(sel.features$fold10$lasso$c))
)## Searching mirecords ...
## Searching mirtarbase ...
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## Searching mirecords ...
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## Searching tarbase ...geneNames## $`3F_0.5_DEV`
## [1] "BCL2" "ERBB2" "AXL" "BAK1" "MYC" "CASP3" "BCL2L11"
## [8] "TP53" "YAP1" "YWHAZ" "STAT3" "PARP1" "XIAP" "CTNNB1"
## [15] "IGF1R" "PRDX1" "PDK1" "PIK3CA" "PRKCA" "MAPK3" "TFRC"
## [22] "TGM2" "MYH9" "CDKN1A" "IRS1" "JUN" "RAF1" "TYMS"
## [29] "FOXO3" "ANXA7" "CLDN7" "CTNNA1" "EIF4G1" "YBX1" "RPS6"
## [36] "SRSF1" "NDRG1" "PECAM1" "YWHAB" "SETD2" "MRE11A" "AKT1"
## [43] "RAD51" "MAPK9" "STMN1" "CHEK1" "ACACA" "WWTR1" "CDK1"
## [50] "EEF2K" "BCL2L1" "FOXM1" "PREX1" "RET" "LCN2" "PTCH1"
## [57] "ANXA1" "SYK"
##
## $`3F_0.5_C`
## [1] "CDKN1A" "MYC" "VHL" "STAT3" "DVL3" "BCL2" "ERBB2"
## [8] "AXL" "BAK1" "CASP3" "BCL2L11" "TP53" "YAP1" "YWHAZ"
## [15] "PARP1" "XIAP" "CTNNB1" "IGF1R" "PRDX1" "PDK1" "PIK3CA"
## [22] "PRKCA" "MAPK3" "TFRC" "TGM2" "NCOA3" "MYH9" "IRS1"
## [29] "JUN" "EZH2" "RAF1" "TYMS" "FOXO3" "ANXA7" "CLDN7"
## [36] "CTNNA1" "EIF4G1" "YBX1" "MAPK8" "RPS6" "SRSF1" "NDRG1"
## [43] "ANLN" "PECAM1" "ERCC1" "YWHAB" "SETD2" "PRKCD" "MRE11A"
## [50] "AKT1" "RAD51" "MAPK9" "TSC2" "STMN1" "CHEK1" "ACACA"
## [57] "WWTR1" "CDK1" "EEF2K" "BCL2L1" "PRKAA1" "FOXM1" "PREX1"
## [64] "RET" "INPP4B" "CASP8" "YWHAE" "LCN2" "PTCH1" "ANXA1"
## [71] "SYK"
##
## $`3F_1_DEV`
## [1] "MAPK3" "CHEK1" "FOXM1" "XIAP" "PREX1" "RET" "TFRC" "ANXA1"
##
## $`3F_1_C`
## [1] "MAPK3" "FOXM1" "XIAP" "TFRC" "ANXA1"
##
## $`5F_0.5_DEV`
## [1] "MRE11A" "AKT1" "RAD51" "MAPK9" "MAPK3" "STMN1" "CHEK1" "ACACA"
## [9] "WWTR1" "CDK1" "EEF2K" "BCL2L1" "TYMS" "FOXM1" "XIAP" "PREX1"
## [17] "RET" "TFRC" "CLDN7" "ANXA1"
##
## $`5F_0.5_C`
## [1] "CDKN1A" "MYC" "VHL" "NOTCH1" "XIAP" "CDK1" "YBX1"
## [8] "BECN1" "STAT3" "DVL3" "PEA15" "AKT1" "ACACA" "BCL2"
## [15] "ERBB2" "AXL" "BAK1" "CASP3" "BCL2L11" "TP53" "YAP1"
## [22] "YWHAZ" "PARP1" "CTNNB1" "IGF1R" "PRDX1" "PDK1" "PIK3CA"
## [29] "PRKCA" "MAPK3" "TFRC" "TGM2" "PTEN" "NCOA3" "MYH9"
## [36] "IRS1" "JUN" "EZH2" "RAF1" "TYMS" "FOXO3" "BCL2L1"
## [43] "ANXA7" "CLDN7" "CTNNA1" "EEF2" "EIF4G1" "GATA3" "GSK3B"
## [50] "MSH6" "NRG1" "MAPK1" "MAPK8" "RPS6" "SRSF1" "TUBA1B"
## [57] "NDRG1" "ANLN" "AKT1S1" "RICTOR" "PECAM1" "ERCC1" "TP53BP1"
## [64] "YWHAB" "SETD2" "GSK3A" "PRKCD" "MRE11A" "RAD51" "MAPK9"
## [71] "TSC2" "STMN1" "CHEK1" "WWTR1" "EEF2K" "E2F1" "CCNB1"
## [78] "PRKAA1" "FOXM1" "PREX1" "RET" "RBM15" "FASN" "INPP4B"
## [85] "XBP1" "MYH11" "CASP8" "RPS6KA1" "YWHAE" "TSC1" "LCN2"
## [92] "TTF1" "LCK" "PTCH1" "ANXA1" "ARID1A" "CASP9" "SYK"
##
## $`5F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP" "PREX1" "RET" "TFRC" "CLDN7" "ANXA1"
##
## $`5F_1_C`
## [1] "ESR1" "MET" "G6PD" "BCL2" "KRAS" "CCND1" "NOTCH3" "AKT1"
## [9] "IGF1R" "FOXO3" "CHEK1" "FN1" "PRKCD" "TGM2" "EEF2K" "TYMS"
## [17] "XIAP" "PREX1" "RET" "TFRC" "CLDN7" "LCN2" "ANXA1"
##
## $`10F_0.5_DEV`
## [1] "CDKN1A" "MYC" "VHL" "BCL2" "ERBB2" "AXL" "BAK1"
## [8] "CASP3" "BCL2L11" "TP53" "YAP1" "YWHAZ" "STAT3" "PARP1"
## [15] "XIAP" "CTNNB1" "IGF1R" "PRDX1" "PDK1" "PIK3CA" "PRKCA"
## [22] "MAPK3" "TFRC" "TGM2" "MYH9" "IRS1" "JUN" "RAF1"
## [29] "TYMS" "FOXO3" "ANXA7" "CLDN7" "CTNNA1" "EIF4G1" "YBX1"
## [36] "RPS6" "SRSF1" "NDRG1" "PECAM1" "YWHAB" "SETD2" "MRE11A"
## [43] "AKT1" "RAD51" "MAPK9" "STMN1" "CHEK1" "ACACA" "WWTR1"
## [50] "CDK1" "EEF2K" "BCL2L1" "FOXM1" "PREX1" "RET" "CASP8"
## [57] "LCN2" "PTCH1" "ANXA1" "SYK"
##
## $`10F_0.5_C`
## [1] "CDKN1A" "MYC" "VHL" "BCL2" "ERBB2" "AXL" "BAK1"
## [8] "CASP3" "BCL2L11" "TP53" "YAP1" "YWHAZ" "STAT3" "PARP1"
## [15] "XIAP" "CTNNB1" "IGF1R" "PRDX1" "PDK1" "PIK3CA" "PRKCA"
## [22] "MAPK3" "TFRC" "TGM2" "MYH9" "IRS1" "JUN" "RAF1"
## [29] "TYMS" "FOXO3" "ANXA7" "CLDN7" "CTNNA1" "EIF4G1" "YBX1"
## [36] "RPS6" "SRSF1" "NDRG1" "PECAM1" "YWHAB" "SETD2" "MRE11A"
## [43] "AKT1" "RAD51" "MAPK9" "STMN1" "CHEK1" "ACACA" "WWTR1"
## [50] "CDK1" "EEF2K" "BCL2L1" "FOXM1" "PREX1" "RET" "CASP8"
## [57] "LCN2" "PTCH1" "ANXA1" "SYK"
##
## $`10F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP" "PREX1" "TFRC" "ANXA1"
##
## $`10F_1_C`
## [1] "CDKN1A" "MYC" "VHL" "AKT1" "MAPK3" "WWTR1" "RAB11B" "TYMS"
## [9] "FOXM1" "XIAP" "PREX1" "RET" "TFRC" "CLDN7" "ANXA1"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet_cox_min.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/58
## GO:0003824 GO:0003824 catalytic activity 25 25/58
## GO:0005198 GO:0005198 structural molecule activity 3 3/58
## GO:0005215 GO:0005215 transporter activity 3 3/58
## GO:0005488 GO:0005488 binding 57 57/58
## GO:0009055 GO:0009055 electron transfer activity 0 0/58
## geneID
## GO:0003774 MYH9
## GO:0003824 ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CDKN1A/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/SYK
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 BCL2/BAK1/IGF1R
## GO:0005488 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 18 18/58
## GO:0002376 GO:0002376 immune system process 33 33/58
## GO:0008152 GO:0008152 metabolic process 51 51/58
## GO:0009987 GO:0009987 cellular process 57 57/58
## GO:0016032 GO:0016032 viral process 7 7/58
## GO:0022414 GO:0022414 reproductive process 17 17/58
## geneID
## GO:0000003 BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/PTCH1
## GO:0002376 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/LCN2/ANXA1/SYK
## GO:0008152 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414 BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/PTCH1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 38 38/58
## GO:0044423 GO:0044423 virion component 0 0/58
## GO:0110165 GO:0110165 cellular anatomical entity 57 57/58
## geneID
## GO:0032991 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/SYK
## GO:0044423
## GO:0110165 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/71
## GO:0003824 GO:0003824 catalytic activity 34 34/71
## GO:0005198 GO:0005198 structural molecule activity 3 3/71
## GO:0005215 GO:0005215 transporter activity 3 3/71
## GO:0005488 GO:0005488 binding 70 70/71
## GO:0009055 GO:0009055 electron transfer activity 0 0/71
## geneID
## GO:0003774 MYH9
## GO:0003824 CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/NCOA3/EZH2/RAF1/TYMS/MAPK8/ERCC1/SETD2/PRKCD/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/PRKAA1/RET/INPP4B/CASP8/SYK
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 20 20/71
## GO:0002376 GO:0002376 immune system process 39 39/71
## GO:0008152 GO:0008152 metabolic process 63 63/71
## GO:0009987 GO:0009987 cellular process 70 70/71
## GO:0016032 GO:0016032 viral process 7 7/71
## GO:0022414 GO:0022414 reproductive process 19 19/71
## geneID
## GO:0000003 STAT3/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/ERCC1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376 CDKN1A/MYC/STAT3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/EZH2/RAF1/FOXO3/MAPK8/NDRG1/PECAM1/ERCC1/SETD2/PRKCD/AKT1/MAPK9/PREX1/RET/CASP8/YWHAE/LCN2/ANXA1/SYK
## GO:0008152 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/CHEK1/ACACA/WWTR1/CDK1/EEF2K/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414 BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/ERCC1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 45 45/71
## GO:0044423 GO:0044423 virion component 0 0/71
## GO:0110165 GO:0110165 cellular anatomical entity 70 70/71
## geneID
## GO:0032991 CDKN1A/MYC/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/ERCC1/AKT1/RAD51/TSC2/CHEK1/WWTR1/CDK1/BCL2L1/PRKAA1/FOXM1/RET/CASP8/SYK
## GO:0044423
## GO:0110165 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 4 4/8
## GO:0005198 GO:0005198 structural molecule activity 0 0/8
## GO:0005215 GO:0005215 transporter activity 0 0/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 MAPK3/CHEK1/XIAP/RET
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/8
## GO:0002376 GO:0002376 immune system process 6 6/8
## GO:0008152 GO:0008152 metabolic process 8 8/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 1 1/8
## GO:0022414 GO:0022414 reproductive process 0 0/8
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 4 4/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 CHEK1/FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/5
## GO:0003824 GO:0003824 catalytic activity 2 2/5
## GO:0005198 GO:0005198 structural molecule activity 0 0/5
## GO:0005215 GO:0005215 transporter activity 0 0/5
## GO:0005488 GO:0005488 binding 5 5/5
## GO:0009055 GO:0009055 electron transfer activity 0 0/5
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/5
## GO:0002376 GO:0002376 immune system process 4 4/5
## GO:0008152 GO:0008152 metabolic process 5 5/5
## GO:0009987 GO:0009987 cellular process 5 5/5
## GO:0016032 GO:0016032 viral process 1 1/5
## GO:0022414 GO:0022414 reproductive process 0 0/5
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/TFRC/ANXA1
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/5
## GO:0044423 GO:0044423 virion component 0 0/5
## GO:0110165 GO:0110165 cellular anatomical entity 5 5/5
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/20
## GO:0003824 GO:0003824 catalytic activity 11 11/20
## GO:0005198 GO:0005198 structural molecule activity 1 1/20
## GO:0005215 GO:0005215 transporter activity 0 0/20
## GO:0005488 GO:0005488 binding 19 19/20
## GO:0009055 GO:0009055 electron transfer activity 0 0/20
## geneID
## GO:0003774
## GO:0003824 AKT1/RAD51/MAPK9/MAPK3/CHEK1/ACACA/CDK1/EEF2K/TYMS/XIAP/RET
## GO:0005198 CLDN7
## GO:0005215
## GO:0005488 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/20
## GO:0002376 GO:0002376 immune system process 8 8/20
## GO:0008152 GO:0008152 metabolic process 16 16/20
## GO:0009987 GO:0009987 cellular process 19 19/20
## GO:0016032 GO:0016032 viral process 3 3/20
## GO:0022414 GO:0022414 reproductive process 4 4/20
## geneID
## GO:0000003 AKT1/RAD51/CDK1/BCL2L1
## GO:0002376 AKT1/MAPK9/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 AKT1/RAD51/MAPK9/MAPK3/CHEK1/ACACA/WWTR1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032 AKT1/CDK1/TFRC
## GO:0022414 AKT1/RAD51/CDK1/BCL2L1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 9 9/20
## GO:0044423 GO:0044423 virion component 0 0/20
## GO:0110165 GO:0110165 cellular anatomical entity 19 19/20
## geneID
## GO:0032991 AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 2 2/98
## GO:0003824 GO:0003824 catalytic activity 45 45/98
## GO:0005198 GO:0005198 structural molecule activity 5 5/98
## GO:0005215 GO:0005215 transporter activity 3 3/98
## GO:0005488 GO:0005488 binding 97 97/98
## GO:0009055 GO:0009055 electron transfer activity 0 0/98
## geneID
## GO:0003774 MYH9/MYH11
## GO:0003824 CDKN1A/VHL/XIAP/CDK1/AKT1/ACACA/ERBB2/AXL/CASP3/PARP1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/PTEN/NCOA3/EZH2/RAF1/TYMS/EEF2/GSK3B/MSH6/MAPK1/MAPK8/TUBA1B/ERCC1/SETD2/GSK3A/PRKCD/RAD51/MAPK9/CHEK1/EEF2K/PRKAA1/RET/FASN/INPP4B/CASP8/RPS6KA1/LCK/CASP9/SYK
## GO:0005198 CLDN7/CTNNA1/RPS6/TUBA1B/MYH11
## GO:0005215 BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 25 25/98
## GO:0002376 GO:0002376 immune system process 50 50/98
## GO:0008152 GO:0008152 metabolic process 87 87/98
## GO:0009987 GO:0009987 cellular process 97 97/98
## GO:0016032 GO:0016032 viral process 11 11/98
## GO:0022414 GO:0022414 reproductive process 24 24/98
## geneID
## GO:0000003 NOTCH1/CDK1/STAT3/AKT1/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/PTEN/MYH9/FOXO3/BCL2L1/CTNNA1/GATA3/MSH6/ERCC1/GSK3A/RAD51/CASP8/PTCH1
## GO:0002376 CDKN1A/MYC/NOTCH1/XIAP/BECN1/STAT3/AKT1/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/EZH2/RAF1/FOXO3/GATA3/MSH6/MAPK1/MAPK8/NDRG1/PECAM1/ERCC1/TP53BP1/SETD2/PRKCD/MAPK9/PREX1/RET/RBM15/XBP1/CASP8/YWHAE/TSC1/LCN2/LCK/ANXA1/ARID1A/SYK
## GO:0008152 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0009987 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0016032 NOTCH1/CDK1/BECN1/AKT1/BCL2/AXL/TP53/TFRC/JUN/GSK3B/GSK3A
## GO:0022414 NOTCH1/CDK1/AKT1/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/PTEN/MYH9/FOXO3/BCL2L1/CTNNA1/GATA3/MSH6/ERCC1/GSK3A/RAD51/CASP8/PTCH1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 64 64/98
## GO:0044423 GO:0044423 virion component 0 0/98
## GO:0110165 GO:0110165 cellular anatomical entity 97 97/98
## geneID
## GO:0032991 CDKN1A/MYC/NOTCH1/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/FOXO3/BCL2L1/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/RPS6/SRSF1/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/GSK3A/RAD51/TSC2/CHEK1/WWTR1/E2F1/CCNB1/PRKAA1/FOXM1/RET/RBM15/XBP1/MYH11/CASP8/TSC1/ARID1A/CASP9/SYK
## GO:0044423
## GO:0110165 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/8
## GO:0003824 GO:0003824 catalytic activity 3 3/8
## GO:0005198 GO:0005198 structural molecule activity 1 1/8
## GO:0005215 GO:0005215 transporter activity 0 0/8
## GO:0005488 GO:0005488 binding 8 8/8
## GO:0009055 GO:0009055 electron transfer activity 0 0/8
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP/RET
## GO:0005198 CLDN7
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/8
## GO:0002376 GO:0002376 immune system process 6 6/8
## GO:0008152 GO:0008152 metabolic process 7 7/8
## GO:0009987 GO:0009987 cellular process 8 8/8
## GO:0016032 GO:0016032 viral process 1 1/8
## GO:0022414 GO:0022414 reproductive process 0 0/8
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/8
## GO:0044423 GO:0044423 virion component 0 0/8
## GO:0110165 GO:0110165 cellular anatomical entity 8 8/8
## geneID
## GO:0032991 FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/23
## GO:0003824 GO:0003824 catalytic activity 13 13/23
## GO:0005198 GO:0005198 structural molecule activity 2 2/23
## GO:0005215 GO:0005215 transporter activity 2 2/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774
## GO:0003824 MET/G6PD/KRAS/CCND1/AKT1/IGF1R/CHEK1/PRKCD/TGM2/EEF2K/TYMS/XIAP/RET
## GO:0005198 FN1/CLDN7
## GO:0005215 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 5 5/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 22 22/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 5 5/23
## geneID
## GO:0000003 ESR1/BCL2/AKT1/IGF1R/FOXO3
## GO:0002376 ESR1/G6PD/BCL2/AKT1/IGF1R/FOXO3/FN1/PRKCD/XIAP/PREX1/RET/TFRC/LCN2/ANXA1
## GO:0008152 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/LCN2/ANXA1
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
## GO:0016032 BCL2/AKT1/TFRC
## GO:0022414 ESR1/BCL2/AKT1/IGF1R/FOXO3
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/TGM2/RET/TFRC
## GO:0044423
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/60
## GO:0003824 GO:0003824 catalytic activity 27 27/60
## GO:0005198 GO:0005198 structural molecule activity 3 3/60
## GO:0005215 GO:0005215 transporter activity 3 3/60
## GO:0005488 GO:0005488 binding 59 59/60
## GO:0009055 GO:0009055 electron transfer activity 0 0/60
## geneID
## GO:0003774 MYH9
## GO:0003824 CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/CASP8/SYK
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/60
## GO:0002376 GO:0002376 immune system process 34 34/60
## GO:0008152 GO:0008152 metabolic process 53 53/60
## GO:0009987 GO:0009987 cellular process 59 59/60
## GO:0016032 GO:0016032 viral process 7 7/60
## GO:0022414 GO:0022414 reproductive process 18 18/60
## geneID
## GO:0000003 BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376 CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/CASP8/LCN2/ANXA1/SYK
## GO:0008152 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414 BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 39 39/60
## GO:0044423 GO:0044423 virion component 0 0/60
## GO:0110165 GO:0110165 cellular anatomical entity 59 59/60
## geneID
## GO:0032991 CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/CASP8/SYK
## GO:0044423
## GO:0110165 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/60
## GO:0003824 GO:0003824 catalytic activity 27 27/60
## GO:0005198 GO:0005198 structural molecule activity 3 3/60
## GO:0005215 GO:0005215 transporter activity 3 3/60
## GO:0005488 GO:0005488 binding 59 59/60
## GO:0009055 GO:0009055 electron transfer activity 0 0/60
## geneID
## GO:0003774 MYH9
## GO:0003824 CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/CASP8/SYK
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/60
## GO:0002376 GO:0002376 immune system process 34 34/60
## GO:0008152 GO:0008152 metabolic process 53 53/60
## GO:0009987 GO:0009987 cellular process 59 59/60
## GO:0016032 GO:0016032 viral process 7 7/60
## GO:0022414 GO:0022414 reproductive process 18 18/60
## geneID
## GO:0000003 BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376 CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/CASP8/LCN2/ANXA1/SYK
## GO:0008152 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414 BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 39 39/60
## GO:0044423 GO:0044423 virion component 0 0/60
## GO:0110165 GO:0110165 cellular anatomical entity 59 59/60
## geneID
## GO:0032991 CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/CASP8/SYK
## GO:0044423
## GO:0110165 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/6
## GO:0003824 GO:0003824 catalytic activity 2 2/6
## GO:0005198 GO:0005198 structural molecule activity 0 0/6
## GO:0005215 GO:0005215 transporter activity 0 0/6
## GO:0005488 GO:0005488 binding 6 6/6
## GO:0009055 GO:0009055 electron transfer activity 0 0/6
## geneID
## GO:0003774
## GO:0003824 MAPK3/XIAP
## GO:0005198
## GO:0005215
## GO:0005488 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/6
## GO:0002376 GO:0002376 immune system process 5 5/6
## GO:0008152 GO:0008152 metabolic process 6 6/6
## GO:0009987 GO:0009987 cellular process 6 6/6
## GO:0016032 GO:0016032 viral process 1 1/6
## GO:0022414 GO:0022414 reproductive process 0 0/6
## geneID
## GO:0000003
## GO:0002376 MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032 TFRC
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/6
## GO:0044423 GO:0044423 virion component 0 0/6
## GO:0110165 GO:0110165 cellular anatomical entity 6 6/6
## geneID
## GO:0032991 FOXM1/TFRC
## GO:0044423
## GO:0110165 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/15
## GO:0003824 GO:0003824 catalytic activity 8 8/15
## GO:0005198 GO:0005198 structural molecule activity 1 1/15
## GO:0005215 GO:0005215 transporter activity 0 0/15
## GO:0005488 GO:0005488 binding 15 15/15
## GO:0009055 GO:0009055 electron transfer activity 0 0/15
## geneID
## GO:0003774
## GO:0003824 CDKN1A/VHL/AKT1/MAPK3/RAB11B/TYMS/XIAP/RET
## GO:0005198 CLDN7
## GO:0005215
## GO:0005488 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/15
## GO:0002376 GO:0002376 immune system process 9 9/15
## GO:0008152 GO:0008152 metabolic process 14 14/15
## GO:0009987 GO:0009987 cellular process 15 15/15
## GO:0016032 GO:0016032 viral process 2 2/15
## GO:0022414 GO:0022414 reproductive process 1 1/15
## geneID
## GO:0000003 AKT1
## GO:0002376 CDKN1A/MYC/AKT1/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032 AKT1/TFRC
## GO:0022414 AKT1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/15
## GO:0044423 GO:0044423 virion component 0 0/15
## GO:0110165 GO:0110165 cellular anatomical entity 15 15/15
## geneID
## GO:0032991 CDKN1A/MYC/AKT1/WWTR1/FOXM1/RET/TFRC
## GO:0044423
## GO:0110165 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_BP[[12]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 10/57
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 5/57
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 10/57
## GO:0051400 GO:0051400 BH domain binding 3/57
## GO:0045296 GO:0045296 cadherin binding 8/57
## GO:0051219 GO:0051219 phosphoprotein binding 5/57
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 6.260798e-07 0.0001582086 8.353543e-05
## GO:0045309 59/18522 1.017419e-06 0.0001582086 8.353543e-05
## GO:0140297 478/18522 1.736820e-06 0.0001781183 9.404791e-05
## GO:0051400 9/18522 2.290911e-06 0.0001781183 9.404791e-05
## GO:0045296 333/18522 7.702656e-06 0.0004791052 2.529714e-04
## GO:0051219 93/18522 9.754331e-06 0.0005055995 2.669606e-04
## geneID Count
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK 10
## GO:0045309 YWHAZ/MAPK3/IRS1/YWHAB/SYK 5
## GO:0140297 BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN 10
## GO:0051400 BCL2/BAK1/BCL2L1 3
## GO:0045296 YWHAZ/CTNNB1/PRDX1/MYH9/CTNNA1/NDRG1/YWHAB/ANXA1 8
## GO:0051219 YWHAZ/MAPK3/IRS1/YWHAB/SYK 5
## ID Description GeneRatio
## GO:0097305 GO:0097305 response to alcohol 16/57
## GO:0010332 GO:0010332 response to gamma radiation 8/57
## GO:2001233 GO:2001233 regulation of apoptotic signaling pathway 14/57
## GO:0010212 GO:0010212 response to ionizing radiation 10/57
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 13/57
## GO:0104004 GO:0104004 cellular response to environmental stimulus 13/57
## BgRatio pvalue p.adjust qvalue
## GO:0097305 259/18888 3.441790e-17 1.106880e-13 4.836620e-14
## GO:0010332 52/18888 2.800084e-12 4.502535e-09 1.967427e-09
## GO:2001233 396/18888 8.562686e-12 7.890099e-09 3.447657e-09
## GO:0010212 138/18888 1.004845e-11 7.890099e-09 3.447657e-09
## GO:0071214 334/18888 1.593278e-11 7.890099e-09 3.447657e-09
## GO:0104004 334/18888 1.593278e-11 7.890099e-09 3.447657e-09
## geneID
## GO:0097305 BAK1/PARP1/CTNNB1/IGF1R/CDKN1A/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/PTCH1
## GO:0010332 BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/BCL2L1
## GO:2001233 BCL2/BAK1/MYC/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212 BCL2/BAK1/MYC/CASP3/TP53/YAP1/PARP1/CDKN1A/RAD51/BCL2L1
## GO:0071214 BAK1/MYC/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/CDKN1A/RAD51/CHEK1/BCL2L1
## GO:0104004 BAK1/MYC/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/CDKN1A/RAD51/CHEK1/BCL2L1
## Count
## GO:0097305 16
## GO:0010332 8
## GO:2001233 14
## GO:0010212 10
## GO:0071214 13
## GO:0104004 13
## ID Description
## GO:0097136 GO:0097136 Bcl-2 family protein complex
## GO:0005901 GO:0005901 caveola
## GO:0044853 GO:0044853 plasma membrane raft
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0045121 GO:0045121 membrane raft
## GO:0098857 GO:0098857 membrane microdomain
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097136 4/57 10/19894 1.255224e-08 3.037641e-06 1.730887e-06
## GO:0005901 6/57 82/19894 1.249512e-07 1.511910e-05 8.615057e-06
## GO:0044853 6/57 113/19894 8.421415e-07 6.793275e-05 3.870896e-05
## GO:0090571 3/57 15/19894 9.901927e-06 5.990666e-04 3.413559e-04
## GO:0045121 7/57 286/19894 1.686241e-05 6.955836e-04 3.963526e-04
## GO:0098857 7/57 287/19894 1.724587e-05 6.955836e-04 3.963526e-04
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1 4
## GO:0005901 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0044853 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0090571 MYC/CTNNB1/FOXO3 3
## GO:0045121 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PECAM1/PTCH1 7
## GO:0098857 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PECAM1/PTCH1 7
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 13/70
## GO:0019902 GO:0019902 phosphatase binding 9/70
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 6/70
## GO:0106310 GO:0106310 protein serine kinase activity 11/70
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 12/70
## GO:0045296 GO:0045296 cadherin binding 10/70
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 6.238592e-09 2.258370e-06 1.090112e-06
## GO:0019902 189/18522 3.770640e-08 6.824858e-06 3.294349e-06
## GO:0045309 59/18522 9.009728e-08 9.808537e-06 4.734566e-06
## GO:0106310 363/18522 1.083816e-07 9.808537e-06 4.734566e-06
## GO:0140297 478/18522 2.081173e-07 1.506770e-05 7.273153e-06
## GO:0045296 333/18522 4.702482e-07 2.837164e-05 1.369495e-05
## geneID
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/MAPK8/PRKCD/AKT1/MAPK9/CHEK1/CDK1/EEF2K/PRKAA1/SYK
## GO:0019902 STAT3/BCL2/TP53/CTNNB1/MAPK3/MAPK8/TSC2/YWHAE/SYK
## GO:0045309 YWHAZ/MAPK3/IRS1/YWHAB/YWHAE/SYK
## GO:0106310 PIK3CA/PRKCA/MAPK3/RAF1/MAPK8/PRKCD/AKT1/MAPK9/CHEK1/CDK1/PRKAA1
## GO:0140297 MYC/VHL/STAT3/BCL2/TP53/YAP1/YWHAZ/PARP1/CTNNB1/MAPK3/NCOA3/JUN
## GO:0045296 YWHAZ/CTNNB1/PRDX1/MYH9/CTNNA1/NDRG1/ANLN/YWHAB/YWHAE/ANXA1
## Count
## GO:0004674 13
## GO:0019902 9
## GO:0045309 6
## GO:0106310 11
## GO:0140297 12
## GO:0045296 10
## ID Description GeneRatio
## GO:0097305 GO:0097305 response to alcohol 18/70
## GO:0000302 GO:0000302 response to reactive oxygen species 15/70
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 17/70
## GO:0104004 GO:0104004 cellular response to environmental stimulus 17/70
## GO:0006979 GO:0006979 response to oxidative stress 18/70
## GO:0062197 GO:0062197 cellular response to chemical stress 16/70
## BgRatio pvalue p.adjust qvalue
## GO:0097305 259/18888 1.992636e-18 6.954300e-15 3.085440e-15
## GO:0000302 203/18888 7.514826e-16 1.311337e-12 5.818058e-13
## GO:0071214 334/18888 3.632063e-15 2.722327e-12 1.207825e-12
## GO:0104004 334/18888 3.632063e-15 2.722327e-12 1.207825e-12
## GO:0006979 398/18888 3.900182e-15 2.722327e-12 1.207825e-12
## GO:0062197 311/18888 2.210193e-14 1.285596e-11 5.703850e-12
## geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/PRKAA1/CASP8/PTCH1
## GO:0000302 BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK8/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
## GO:0071214 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/MAPK8/ERCC1/PRKCD/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/MAPK8/ERCC1/PRKCD/RAD51/CHEK1/BCL2L1/CASP8
## GO:0006979 BCL2/AXL/BAK1/CASP3/TP53/PARP1/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK8/ERCC1/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
## GO:0062197 AXL/CASP3/TP53/PARP1/PRDX1/PIK3CA/MAPK3/JUN/EZH2/FOXO3/MAPK8/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
## Count
## GO:0097305 18
## GO:0000302 15
## GO:0071214 17
## GO:0104004 17
## GO:0006979 18
## GO:0062197 16
## ID Description
## GO:0097136 GO:0097136 Bcl-2 family protein complex
## GO:0005901 GO:0005901 caveola
## GO:0044853 GO:0044853 plasma membrane raft
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0005925 GO:0005925 focal adhesion
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097136 4/70 10/19894 2.904473e-08 7.754944e-06 4.647157e-06
## GO:0005901 6/70 82/19894 4.326477e-07 5.775846e-05 3.461181e-05
## GO:0044853 6/70 113/19894 2.865901e-06 2.550652e-04 1.528481e-04
## GO:0005741 7/70 219/19894 1.184844e-05 7.451852e-04 4.465529e-04
## GO:0005925 9/70 421/19894 1.622931e-05 7.451852e-04 4.465529e-04
## GO:0090571 3/70 15/19894 1.841593e-05 7.451852e-04 4.465529e-04
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1 4
## GO:0005901 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0044853 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0005741 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## GO:0005925 YWHAZ/CTNNB1/MAPK3/TGM2/MYH9/CTNNA1/YWHAB/YWHAE/ANXA1 9
## GO:0090571 MYC/CTNNB1/FOXO3 3
## ID Description GeneRatio
## GO:0004998 GO:0004998 transferrin receptor activity 1/8
## GO:0035402 GO:0035402 histone H3T11 kinase activity 1/8
## GO:0019834 GO:0019834 phospholipase A2 inhibitor activity 1/8
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 1/8
## GO:0004859 GO:0004859 phospholipase inhibitor activity 1/8
## GO:0140996 GO:0140996 histone H3 kinase activity 1/8
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 2/18522 0.0008636744 0.02288737 0.009091309 TFRC 1
## GO:0035402 2/18522 0.0008636744 0.02288737 0.009091309 CHEK1 1
## GO:0019834 4/18522 0.0017266959 0.03050496 0.012117165 ANXA1 1
## GO:0120283 7/18522 0.0030200053 0.04001507 0.015894765 XIAP 1
## GO:0004859 11/18522 0.0047421371 0.04188888 0.016639078 ANXA1 1
## GO:0140996 11/18522 0.0047421371 0.04188888 0.016639078 CHEK1 1
## ID Description GeneRatio
## GO:0050900 GO:0050900 leukocyte migration 4/8
## GO:0071621 GO:0071621 granulocyte chemotaxis 3/8
## GO:0045785 GO:0045785 positive regulation of cell adhesion 4/8
## GO:0097530 GO:0097530 granulocyte migration 3/8
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation 3/8
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 3/8
## BgRatio pvalue p.adjust qvalue geneID
## GO:0050900 396/18888 1.246268e-05 0.005166253 0.002253057 MAPK3/PREX1/RET/ANXA1
## GO:0071621 128/18888 1.660669e-05 0.005166253 0.002253057 MAPK3/PREX1/ANXA1
## GO:0045785 485/18888 2.769198e-05 0.005166253 0.002253057 PREX1/RET/TFRC/ANXA1
## GO:0097530 154/18888 2.888705e-05 0.005166253 0.002253057 MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 3.486001e-05 0.005166253 0.002253057 MAPK3/TFRC/ANXA1
## GO:0042770 188/18888 5.238574e-05 0.006369700 0.002777893 MAPK3/CHEK1/FOXM1
## Count
## GO:0050900 4
## GO:0071621 3
## GO:0045785 4
## GO:0097530 3
## GO:0070665 3
## GO:0042770 3
## ID Description GeneRatio BgRatio pvalue
## GO:0005769 GO:0005769 early endosome 4/8 428/19894 1.380895e-05
## p.adjust qvalue geneID Count
## GO:0005769 0.0007456833 0.0004506078 MAPK3/RET/TFRC/ANXA1 4
## ID Description GeneRatio
## GO:0004998 GO:0004998 transferrin receptor activity 1/5
## GO:0019834 GO:0019834 phospholipase A2 inhibitor activity 1/5
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 1/5
## GO:0004859 GO:0004859 phospholipase inhibitor activity 1/5
## GO:0055102 GO:0055102 lipase inhibitor activity 1/5
## GO:0004857 GO:0004857 enzyme inhibitor activity 2/5
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 2/18522 0.0005398402 0.02266839 0.006249431 TFRC 1
## GO:0019834 4/18522 0.0010794472 0.02266839 0.006249431 ANXA1 1
## GO:0120283 7/18522 0.0018884208 0.02514362 0.006931825 XIAP 1
## GO:0004859 11/18522 0.0029662367 0.02514362 0.006931825 ANXA1 1
## GO:0055102 15/18522 0.0040431214 0.02514362 0.006931825 ANXA1 1
## GO:0004857 389/18522 0.0042187412 0.02514362 0.006931825 XIAP/ANXA1 2
## ID
## GO:0070665 GO:0070665
## GO:0070663 GO:0070663
## GO:0032872 GO:0032872
## GO:0051054 GO:0051054
## GO:0070302 GO:0070302
## GO:0070661 GO:0070661
## Description
## GO:0070665 positive regulation of leukocyte proliferation
## GO:0070663 regulation of leukocyte proliferation
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0051054 positive regulation of DNA metabolic process
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0070661 leukocyte proliferation
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0070665 3/5 164/18888 6.345810e-06 0.003540962 0.001035369
## GO:0070663 3/5 267/18888 2.735257e-05 0.004381714 0.001281203
## GO:0032872 2/5 35/18888 3.324142e-05 0.004381714 0.001281203
## GO:0051054 3/5 301/18888 3.913209e-05 0.004381714 0.001281203
## GO:0070302 2/5 38/18888 3.926267e-05 0.004381714 0.001281203
## GO:0070661 3/5 352/18888 6.241821e-05 0.005446835 0.001592642
## geneID Count
## GO:0070665 MAPK3/TFRC/ANXA1 3
## GO:0070663 MAPK3/TFRC/ANXA1 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0051054 MAPK3/FOXM1/TFRC 3
## GO:0070302 MAPK3/FOXM1 2
## GO:0070661 MAPK3/TFRC/ANXA1 3
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 3/5 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 2/5 255/19894
## GO:0009925 GO:0009925 basal plasma membrane 2/5 286/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/5 8/19894
## GO:0045178 GO:0045178 basal part of cell 2/5 305/19894
## GO:0005925 GO:0005925 focal adhesion 2/5 421/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 9.575381e-05 0.004117414 0.001814283 MAPK3/TFRC/ANXA1 3
## GO:0016323 1.595396e-03 0.019541951 0.008610897 TFRC/ANXA1 2
## GO:0009925 2.001441e-03 0.019541951 0.008610897 TFRC/ANXA1 2
## GO:1990712 2.009242e-03 0.019541951 0.008610897 TFRC 1
## GO:0045178 2.272320e-03 0.019541951 0.008610897 TFRC/ANXA1 2
## GO:0005925 4.282683e-03 0.024274850 0.010696384 MAPK3/ANXA1 2
## ID Description
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004707 GO:0004707 MAP kinase activity
## GO:0035173 GO:0035173 histone kinase activity
## GO:0004712 GO:0004712 protein serine/threonine/tyrosine kinase activity
## GO:0030544 GO:0030544 Hsp70 protein binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004674 6/19 427/18522 3.048491e-06 0.000353625 0.0001829095
## GO:0106310 5/19 363/18522 2.608195e-05 0.001512753 0.0007824586
## GO:0004707 2/19 16/18522 1.186135e-04 0.004586388 0.0023722695
## GO:0035173 2/19 23/18522 2.490081e-04 0.007221236 0.0037351219
## GO:0004712 2/19 43/18522 8.779498e-04 0.020368435 0.0105353976
## GO:0030544 2/19 51/18522 1.233584e-03 0.023787161 0.0123037041
## geneID Count
## GO:0004674 AKT1/MAPK9/MAPK3/CHEK1/CDK1/EEF2K 6
## GO:0106310 AKT1/MAPK9/MAPK3/CHEK1/CDK1 5
## GO:0004707 MAPK9/MAPK3 2
## GO:0035173 CHEK1/CDK1 2
## GO:0004712 AKT1/MAPK9 2
## GO:0030544 CDK1/TFRC 2
## ID Description
## GO:0097305 GO:0097305 response to alcohol
## GO:0046686 GO:0046686 response to cadmium ion
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process
## GO:0042770 GO:0042770 signal transduction in response to DNA damage
## GO:0010038 GO:0010038 response to metal ion
## GO:1900182 GO:1900182 positive regulation of protein localization to nucleus
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097305 7/19 259/18888 3.680634e-09 5.675538e-06 2.704298e-06
## GO:0046686 4/19 60/18888 3.440463e-07 1.825118e-04 8.696376e-05
## GO:0051054 6/19 301/18888 3.550813e-07 1.825118e-04 8.696376e-05
## GO:0042770 5/19 188/18888 9.617566e-07 3.119988e-04 1.486621e-04
## GO:0010038 6/19 360/18888 1.011669e-06 3.119988e-04 1.486621e-04
## GO:1900182 4/19 94/18888 2.105488e-06 5.411104e-04 2.578299e-04
## geneID Count
## GO:0097305 AKT1/RAD51/ACACA/CDK1/BCL2L1/TYMS/CLDN7 7
## GO:0046686 AKT1/MAPK9/MAPK3/CDK1 4
## GO:0051054 AKT1/RAD51/MAPK3/CDK1/FOXM1/TFRC 6
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1 5
## GO:0010038 AKT1/MAPK9/MAPK3/CDK1/EEF2K/TFRC 6
## GO:1900182 AKT1/WWTR1/CDK1/TFRC 4
## ID Description GeneRatio BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 3/19 173/19894
## GO:0005769 GO:0005769 early endosome 4/19 428/19894
## GO:0005759 GO:0005759 mitochondrial matrix 4/19 491/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 3/19 255/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/19 68/19894
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/19 2/19894
## pvalue p.adjust qvalue geneID Count
## GO:0000781 0.0005652514 0.025775 0.02034869 RAD51/CHEK1/CDK1 3
## GO:0005769 0.0006335653 0.025775 0.02034869 MAPK3/RET/TFRC/ANXA1 4
## GO:0005759 0.0010580319 0.025775 0.02034869 RAD51/CDK1/BCL2L1/TYMS 4
## GO:0016323 0.0017325255 0.025775 0.02034869 TFRC/CLDN7/ANXA1 3
## GO:0016328 0.0018960073 0.025775 0.02034869 CLDN7/ANXA1 2
## GO:0097122 0.0019092595 0.025775 0.02034869 CDK1 1
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 17/97
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 17/97
## GO:0106310 GO:0106310 protein serine kinase activity 15/97
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 8/97
## GO:0019902 GO:0019902 phosphatase binding 11/97
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 13/97
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 7.461099e-11 3.357494e-08 1.743541e-08
## GO:0140297 478/18522 4.254302e-10 8.448519e-08 4.387301e-08
## GO:0106310 363/18522 6.535172e-10 8.448519e-08 4.387301e-08
## GO:0045309 59/18522 7.509794e-10 8.448519e-08 4.387301e-08
## GO:0019902 189/18522 4.327426e-09 3.894684e-07 2.022502e-07
## GO:0044389 324/18522 1.408341e-08 1.056256e-06 5.485118e-07
## geneID
## GO:0004674 CDK1/AKT1/PIK3CA/PRKCA/MAPK3/RAF1/GSK3B/MAPK1/MAPK8/GSK3A/PRKCD/MAPK9/CHEK1/EEF2K/PRKAA1/RPS6KA1/SYK
## GO:0140297 MYC/VHL/STAT3/BCL2/TP53/YAP1/YWHAZ/PARP1/CTNNB1/MAPK3/NCOA3/JUN/GATA3/GSK3B/TP53BP1/E2F1/ARID1A
## GO:0106310 CDK1/AKT1/PIK3CA/PRKCA/MAPK3/RAF1/GSK3B/MAPK1/MAPK8/GSK3A/PRKCD/MAPK9/CHEK1/PRKAA1/RPS6KA1
## GO:0045309 YWHAZ/MAPK3/IRS1/MAPK1/YWHAB/YWHAE/LCK/SYK
## GO:0019902 STAT3/BCL2/TP53/CTNNB1/MAPK3/MAPK1/MAPK8/TSC2/YWHAE/LCK/SYK
## GO:0044389 CDKN1A/BECN1/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/GSK3B/TUBA1B/CCNB1/CASP8/YWHAE
## Count
## GO:0004674 17
## GO:0140297 17
## GO:0106310 15
## GO:0045309 8
## GO:0019902 11
## GO:0044389 13
## ID Description GeneRatio
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 21/97
## GO:0104004 GO:0104004 cellular response to environmental stimulus 21/97
## GO:0031929 GO:0031929 TOR signaling 16/97
## GO:0018105 GO:0018105 peptidyl-serine phosphorylation 19/97
## GO:0000302 GO:0000302 response to reactive oxygen species 17/97
## GO:0071496 GO:0071496 cellular response to external stimulus 20/97
## BgRatio pvalue p.adjust qvalue
## GO:0071214 334/18888 2.494398e-17 5.106032e-14 2.305348e-14
## GO:0104004 334/18888 2.494398e-17 5.106032e-14 2.305348e-14
## GO:0031929 165/18888 2.365810e-16 2.520865e-13 1.138158e-13
## GO:0018105 282/18888 2.716733e-16 2.520865e-13 1.138158e-13
## GO:0000302 203/18888 3.078731e-16 2.520865e-13 1.138158e-13
## GO:0071496 335/18888 4.257721e-16 2.905185e-13 1.311677e-13
## geneID
## GO:0071214 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/PTEN/BCL2L1/GATA3/MAPK8/ERCC1/TP53BP1/PRKCD/RAD51/CHEK1/CASP8/CASP9
## GO:0104004 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/PTEN/BCL2L1/GATA3/MAPK8/ERCC1/TP53BP1/PRKCD/RAD51/CHEK1/CASP8/CASP9
## GO:0031929 VHL/AKT1/YWHAZ/PIK3CA/MAPK3/GATA3/GSK3B/RPS6/AKT1S1/RICTOR/GSK3A/TSC2/PRKAA1/RPS6KA1/TSC1/SYK
## GO:0018105 CDK1/AKT1/BCL2/BAK1/PRKCA/TFRC/PTEN/RAF1/EIF4G1/GSK3B/MAPK1/MAPK8/RICTOR/GSK3A/PRKCD/MAPK9/PRKAA1/RET/RPS6KA1
## GO:0000302 CDK1/BECN1/AKT1/BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK1/MAPK8/PRKCD/MAPK9/PRKAA1
## GO:0071496 CDKN1A/BECN1/BCL2/AXL/BAK1/TP53/YWHAZ/IGF1R/MAPK3/FOXO3/EIF4G1/MAPK1/MAPK8/RICTOR/TSC2/CHEK1/PRKAA1/XBP1/CASP8/TSC1
## Count
## GO:0071214 21
## GO:0104004 21
## GO:0031929 16
## GO:0018105 19
## GO:0000302 17
## GO:0071496 20
## ID Description GeneRatio BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex 4/97 10/19894
## GO:0005901 GO:0005901 caveola 7/97 82/19894
## GO:0042470 GO:0042470 melanosome 7/97 112/19894
## GO:0048770 GO:0048770 pigment granule 7/97 112/19894
## GO:0044853 GO:0044853 plasma membrane raft 7/97 113/19894
## GO:0045121 GO:0045121 membrane raft 9/97 286/19894
## pvalue p.adjust qvalue
## GO:0097136 1.090420e-07 2.337397e-05 1.468440e-05
## GO:0005901 1.484062e-07 2.337397e-05 1.468440e-05
## GO:0042470 1.255778e-06 8.400528e-05 5.277525e-05
## GO:0048770 1.255778e-06 8.400528e-05 5.277525e-05
## GO:0044853 1.333417e-06 8.400528e-05 5.277525e-05
## GO:0045121 1.094424e-05 4.659951e-04 2.927555e-04
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1 4
## GO:0005901 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PTCH1 7
## GO:0042470 YWHAZ/PRDX1/TFRC/YWHAB/FASN/MYH11/YWHAE 7
## GO:0048770 YWHAZ/PRDX1/TFRC/YWHAB/FASN/MYH11/YWHAE 7
## GO:0044853 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PTCH1 7
## GO:0045121 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PECAM1/LCK/PTCH1 9
## ID Description GeneRatio BgRatio
## GO:0004998 GO:0004998 transferrin receptor activity 1/8 2/18522
## GO:0019834 GO:0019834 phospholipase A2 inhibitor activity 1/8 4/18522
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 1/8 7/18522
## pvalue p.adjust qvalue geneID Count
## GO:0004998 0.0008636744 0.04230405 0.01908453 TFRC 1
## GO:0019834 0.0017266959 0.04230405 0.01908453 ANXA1 1
## GO:0120283 0.0030200053 0.04932675 0.02225267 XIAP 1
## ID Description GeneRatio
## GO:0050900 GO:0050900 leukocyte migration 4/8
## GO:0071621 GO:0071621 granulocyte chemotaxis 3/8
## GO:0045785 GO:0045785 positive regulation of cell adhesion 4/8
## GO:0097530 GO:0097530 granulocyte migration 3/8
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation 3/8
## GO:0002520 GO:0002520 immune system development 3/8
## BgRatio pvalue p.adjust qvalue geneID
## GO:0050900 396/18888 1.246268e-05 0.004831597 0.002194346 MAPK3/PREX1/RET/ANXA1
## GO:0071621 128/18888 1.660669e-05 0.004831597 0.002194346 MAPK3/PREX1/ANXA1
## GO:0045785 485/18888 2.769198e-05 0.004831597 0.002194346 PREX1/RET/TFRC/ANXA1
## GO:0097530 154/18888 2.888705e-05 0.004831597 0.002194346 MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 3.486001e-05 0.004831597 0.002194346 MAPK3/TFRC/ANXA1
## GO:0002520 197/18888 6.021118e-05 0.006808100 0.003092006 MAPK3/RET/TFRC
## Count
## GO:0050900 4
## GO:0071621 3
## GO:0045785 4
## GO:0097530 3
## GO:0070665 3
## GO:0002520 3
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 4/8 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 3/8 255/19894
## GO:0009925 GO:0009925 basal plasma membrane 3/8 286/19894
## GO:0045178 GO:0045178 basal part of cell 3/8 305/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/8 68/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/8 8/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 1.380895e-05 0.0007180654 0.0004215363 MAPK3/RET/TFRC/ANXA1 4
## GO:0016323 1.111412e-04 0.0024536609 0.0014404082 TFRC/CLDN7/ANXA1 3
## GO:0009925 1.560820e-04 0.0024536609 0.0014404082 TFRC/CLDN7/ANXA1 3
## GO:0045178 1.887431e-04 0.0024536609 0.0014404082 TFRC/CLDN7/ANXA1 3
## GO:0016328 3.180919e-04 0.0033081558 0.0019420348 CLDN7/ANXA1 2
## GO:1990712 3.213091e-03 0.0278467858 0.0163473034 TFRC 1
## ID Description
## GO:0004713 GO:0004713 protein tyrosine kinase activity
## GO:0030235 GO:0030235 nitric-oxide synthase regulator activity
## GO:0004714 GO:0004714 transmembrane receptor protein tyrosine kinase activity
## GO:0043560 GO:0043560 insulin receptor substrate binding
## GO:0019199 GO:0019199 transmembrane receptor protein kinase activity
## GO:0071889 GO:0071889 14-3-3 protein binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004713 4/23 138/18522 2.340073e-05 0.002777270 0.001575410
## GO:0030235 2/23 7/18522 3.085855e-05 0.002777270 0.001575410
## GO:0004714 3/23 60/18522 5.465172e-05 0.003279103 0.001860076
## GO:0043560 2/23 13/18522 1.140988e-04 0.004477197 0.002539697
## GO:0019199 3/23 79/18522 1.243666e-04 0.004477197 0.002539697
## GO:0071889 2/23 32/18522 7.152122e-04 0.021456366 0.012171155
## geneID Count
## GO:0004713 MET/IGF1R/PRKCD/RET 4
## GO:0030235 ESR1/AKT1 2
## GO:0004714 MET/IGF1R/RET 3
## GO:0043560 IGF1R/PRKCD 2
## GO:0019199 MET/IGF1R/RET 3
## GO:0071889 ESR1/AKT1 2
## ID Description GeneRatio
## GO:0010720 GO:0010720 positive regulation of cell development 8/23
## GO:0045785 GO:0045785 positive regulation of cell adhesion 8/23
## GO:0048872 GO:0048872 homeostasis of number of cells 7/23
## GO:0051384 GO:0051384 response to glucocorticoid 5/23
## GO:0097305 GO:0097305 response to alcohol 6/23
## GO:0048732 GO:0048732 gland development 7/23
## BgRatio pvalue p.adjust qvalue
## GO:0010720 454/18888 3.742111e-08 4.945373e-05 2.099872e-05
## GO:0045785 485/18888 6.232344e-08 4.945373e-05 2.099872e-05
## GO:0048872 322/18888 7.604366e-08 4.945373e-05 2.099872e-05
## GO:0051384 134/18888 5.063281e-07 2.032025e-04 8.628255e-05
## GO:0097305 259/18888 5.207650e-07 2.032025e-04 8.628255e-05
## GO:0048732 449/18888 7.218445e-07 2.227905e-04 9.459987e-05
## geneID Count
## GO:0010720 BCL2/KRAS/FOXO3/FN1/TGM2/EEF2K/RET/ANXA1 8
## GO:0045785 AKT1/FOXO3/FN1/TGM2/PREX1/RET/TFRC/ANXA1 8
## GO:0048872 G6PD/BCL2/KRAS/AKT1/FOXO3/XIAP/ANXA1 7
## GO:0051384 BCL2/IGF1R/FOXO3/TYMS/ANXA1 5
## GO:0097305 G6PD/AKT1/IGF1R/FOXO3/TYMS/CLDN7 6
## GO:0048732 ESR1/MET/BCL2/CCND1/AKT1/TGM2/TYMS 7
## ID Description GeneRatio BgRatio
## GO:0009925 GO:0009925 basal plasma membrane 4/23 286/19894
## GO:0045178 GO:0045178 basal part of cell 4/23 305/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 3/23 219/19894
## GO:0097128 GO:0097128 cyclin D1-CDK4 complex 1/23 2/19894
## GO:0097138 GO:0097138 BAD-BCL-2 complex 1/23 2/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/23 68/19894
## pvalue p.adjust qvalue geneID Count
## GO:0009925 0.0002985362 0.02076713 0.01443972 MET/TFRC/CLDN7/ANXA1 4
## GO:0045178 0.0003810483 0.02076713 0.01443972 MET/TFRC/CLDN7/ANXA1 4
## GO:0005741 0.0019805936 0.03692764 0.02567639 BCL2/KRAS/FOXO3 3
## GO:0097128 0.0023109764 0.03692764 0.02567639 CCND1 1
## GO:0097138 0.0023109764 0.03692764 0.02567639 BCL2 1
## GO:0016328 0.0027805761 0.03692764 0.02567639 CLDN7/ANXA1 2
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 11/59
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 10/59
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 5/59
## GO:0051400 GO:0051400 BH domain binding 3/59
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 8/59
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 8/59
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 2.758963e-07 8.718322e-05 4.501465e-05
## GO:0004674 427/18522 8.742183e-07 1.275162e-04 6.583946e-05
## GO:0045309 59/18522 1.210596e-06 1.275162e-04 6.583946e-05
## GO:0051400 9/18522 2.544052e-06 2.009801e-04 1.037706e-04
## GO:0031625 305/18522 5.275026e-06 3.333817e-04 1.721324e-04
## GO:0044389 324/18522 8.207994e-06 4.322877e-04 2.231998e-04
## geneID Count
## GO:0140297 MYC/VHL/BCL2/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN 11
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK 10
## GO:0045309 YWHAZ/MAPK3/IRS1/YWHAB/SYK 5
## GO:0051400 BCL2/BAK1/BCL2L1 3
## GO:0031625 CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8 8
## GO:0044389 CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8 8
## ID Description GeneRatio
## GO:0097305 GO:0097305 response to alcohol 17/59
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 14/59
## GO:0104004 GO:0104004 cellular response to environmental stimulus 14/59
## GO:0010332 GO:0010332 response to gamma radiation 8/59
## GO:2001233 GO:2001233 regulation of apoptotic signaling pathway 14/59
## GO:0010212 GO:0010212 response to ionizing radiation 10/59
## BgRatio pvalue p.adjust qvalue
## GO:0097305 259/18888 2.098797e-18 6.774918e-15 2.969246e-15
## GO:0071214 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0104004 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0010332 52/18888 3.742034e-12 3.019822e-09 1.323498e-09
## GO:2001233 396/18888 1.424590e-11 7.768814e-09 3.404841e-09
## GO:0010212 138/18888 1.444018e-11 7.768814e-09 3.404841e-09
## geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/CASP8/PTCH1
## GO:0071214 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0010332 CDKN1A/MYC/BCL2/BAK1/TP53/YAP1/PARP1/BCL2L1
## GO:2001233 MYC/BCL2/BAK1/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212 CDKN1A/MYC/BCL2/BAK1/CASP3/TP53/YAP1/PARP1/RAD51/BCL2L1
## Count
## GO:0097305 17
## GO:0071214 14
## GO:0104004 14
## GO:0010332 8
## GO:2001233 14
## GO:0010212 10
## ID Description GeneRatio BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex 4/59 10/19894
## GO:0005901 GO:0005901 caveola 6/59 82/19894
## GO:0044853 GO:0044853 plasma membrane raft 6/59 113/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 7/59 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 7/59 248/19894
## GO:0019867 GO:0019867 outer membrane 7/59 250/19894
## pvalue p.adjust qvalue
## GO:0097136 1.445555e-08 3.527155e-06 1.993345e-06
## GO:0005901 1.541329e-07 1.880421e-05 1.062706e-05
## GO:0044853 1.036054e-06 8.426574e-05 4.762214e-05
## GO:0005741 3.735501e-06 2.278656e-04 1.287765e-04
## GO:0031968 8.442607e-06 3.617766e-04 2.044553e-04
## GO:0019867 8.896146e-06 3.617766e-04 2.044553e-04
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1 4
## GO:0005901 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0044853 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0005741 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## GO:0031968 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## GO:0019867 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 11/59
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 10/59
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 5/59
## GO:0051400 GO:0051400 BH domain binding 3/59
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 8/59
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 8/59
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 2.758963e-07 8.718322e-05 4.501465e-05
## GO:0004674 427/18522 8.742183e-07 1.275162e-04 6.583946e-05
## GO:0045309 59/18522 1.210596e-06 1.275162e-04 6.583946e-05
## GO:0051400 9/18522 2.544052e-06 2.009801e-04 1.037706e-04
## GO:0031625 305/18522 5.275026e-06 3.333817e-04 1.721324e-04
## GO:0044389 324/18522 8.207994e-06 4.322877e-04 2.231998e-04
## geneID Count
## GO:0140297 MYC/VHL/BCL2/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN 11
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK 10
## GO:0045309 YWHAZ/MAPK3/IRS1/YWHAB/SYK 5
## GO:0051400 BCL2/BAK1/BCL2L1 3
## GO:0031625 CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8 8
## GO:0044389 CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8 8
## ID Description GeneRatio
## GO:0097305 GO:0097305 response to alcohol 17/59
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 14/59
## GO:0104004 GO:0104004 cellular response to environmental stimulus 14/59
## GO:0010332 GO:0010332 response to gamma radiation 8/59
## GO:2001233 GO:2001233 regulation of apoptotic signaling pathway 14/59
## GO:0010212 GO:0010212 response to ionizing radiation 10/59
## BgRatio pvalue p.adjust qvalue
## GO:0097305 259/18888 2.098797e-18 6.774918e-15 2.969246e-15
## GO:0071214 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0104004 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0010332 52/18888 3.742034e-12 3.019822e-09 1.323498e-09
## GO:2001233 396/18888 1.424590e-11 7.768814e-09 3.404841e-09
## GO:0010212 138/18888 1.444018e-11 7.768814e-09 3.404841e-09
## geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/CASP8/PTCH1
## GO:0071214 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0010332 CDKN1A/MYC/BCL2/BAK1/TP53/YAP1/PARP1/BCL2L1
## GO:2001233 MYC/BCL2/BAK1/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212 CDKN1A/MYC/BCL2/BAK1/CASP3/TP53/YAP1/PARP1/RAD51/BCL2L1
## Count
## GO:0097305 17
## GO:0071214 14
## GO:0104004 14
## GO:0010332 8
## GO:2001233 14
## GO:0010212 10
## ID Description GeneRatio BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex 4/59 10/19894
## GO:0005901 GO:0005901 caveola 6/59 82/19894
## GO:0044853 GO:0044853 plasma membrane raft 6/59 113/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 7/59 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 7/59 248/19894
## GO:0019867 GO:0019867 outer membrane 7/59 250/19894
## pvalue p.adjust qvalue
## GO:0097136 1.445555e-08 3.527155e-06 1.993345e-06
## GO:0005901 1.541329e-07 1.880421e-05 1.062706e-05
## GO:0044853 1.036054e-06 8.426574e-05 4.762214e-05
## GO:0005741 3.735501e-06 2.278656e-04 1.287765e-04
## GO:0031968 8.442607e-06 3.617766e-04 2.044553e-04
## GO:0019867 8.896146e-06 3.617766e-04 2.044553e-04
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1 4
## GO:0005901 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0044853 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1 6
## GO:0005741 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## GO:0031968 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## GO:0019867 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8 7
## ID Description GeneRatio
## GO:0004998 GO:0004998 transferrin receptor activity 1/6
## GO:0019834 GO:0019834 phospholipase A2 inhibitor activity 1/6
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 1/6
## GO:0004859 GO:0004859 phospholipase inhibitor activity 1/6
## GO:0055102 GO:0055102 lipase inhibitor activity 1/6
## GO:0004707 GO:0004707 MAP kinase activity 1/6
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004998 2/18522 0.0006477907 0.02979033 0.01227062 TFRC 1
## GO:0019834 4/18522 0.0012952318 0.02979033 0.01227062 ANXA1 1
## GO:0120283 7/18522 0.0022657379 0.03302896 0.01360461 XIAP 1
## GO:0004859 11/18522 0.0035585234 0.03302896 0.01360461 ANXA1 1
## GO:0055102 15/18522 0.0048499126 0.03302896 0.01360461 ANXA1 1
## GO:0004707 16/18522 0.0051725419 0.03302896 0.01360461 MAPK3 1
## ID Description GeneRatio
## GO:0071621 GO:0071621 granulocyte chemotaxis 3/6
## GO:0097530 GO:0097530 granulocyte migration 3/6
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation 3/6
## GO:0030595 GO:0030595 leukocyte chemotaxis 3/6
## GO:0097529 GO:0097529 myeloid leukocyte migration 3/6
## GO:0032872 GO:0032872 regulation of stress-activated MAPK cascade 2/6
## BgRatio pvalue p.adjust qvalue geneID
## GO:0071621 128/18888 5.990226e-06 0.002463257 0.0008761002 MAPK3/PREX1/ANXA1
## GO:0097530 154/18888 1.044150e-05 0.002463257 0.0008761002 MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 1.261053e-05 0.002463257 0.0008761002 MAPK3/TFRC/ANXA1
## GO:0030595 237/18888 3.794128e-05 0.004308506 0.0015323947 MAPK3/PREX1/ANXA1
## GO:0097529 239/18888 3.890475e-05 0.004308506 0.0015323947 MAPK3/PREX1/ANXA1
## GO:0032872 35/18888 4.980407e-05 0.004308506 0.0015323947 MAPK3/FOXM1
## Count
## GO:0071621 3
## GO:0097530 3
## GO:0070665 3
## GO:0030595 3
## GO:0097529 3
## GO:0032872 2
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 3/6 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 2/6 255/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex 1/6 8/19894
## GO:0009925 GO:0009925 basal plasma membrane 2/6 286/19894
## GO:0045178 GO:0045178 basal part of cell 2/6 305/19894
## GO:0031143 GO:0031143 pseudopodium 1/6 18/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 0.0001884452 0.008856923 0.00416563 MAPK3/TFRC/ANXA1 3
## GO:0016323 0.0023728661 0.031715571 0.01491662 TFRC/ANXA1 2
## GO:1990712 0.0024106661 0.031715571 0.01491662 TFRC 1
## GO:0009925 0.0029736864 0.031715571 0.01491662 TFRC/ANXA1 2
## GO:0045178 0.0033739969 0.031715571 0.01491662 TFRC/ANXA1 2
## GO:0031143 0.0054171867 0.038952261 0.01832021 MAPK3 1
## ID Description
## GO:0004857 GO:0004857 enzyme inhibitor activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0004860 GO:0004860 protein kinase inhibitor activity
## GO:0004998 GO:0004998 transferrin receptor activity
## GO:0019210 GO:0019210 kinase inhibitor activity
## GO:0072341 GO:0072341 modified amino acid binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004857 4/15 389/18522 0.0002176436 0.02205928 0.01245452
## GO:0030291 2/15 37/18522 0.0004010778 0.02205928 0.01245452
## GO:0004860 2/15 73/18522 0.0015562116 0.03903069 0.02203647
## GO:0004998 1/15 2/18522 0.0016190833 0.03903069 0.02203647
## GO:0019210 2/15 78/18522 0.0017741224 0.03903069 0.02203647
## GO:0072341 2/15 101/18522 0.0029515609 0.04762216 0.02688715
## geneID Count
## GO:0004857 CDKN1A/AKT1/XIAP/ANXA1 4
## GO:0030291 CDKN1A/AKT1 2
## GO:0004860 CDKN1A/AKT1 2
## GO:0004998 TFRC 1
## GO:0019210 CDKN1A/AKT1 2
## GO:0072341 TYMS/ANXA1 2
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0070482 GO:0070482
## GO:0070665 GO:0070665
## GO:0051347 GO:0051347
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0070482 response to oxygen levels
## GO:0070665 positive regulation of leukocyte proliferation
## GO:0051347 positive regulation of transferase activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 6/15 301/18888 6.912116e-08 9.511072e-05 3.870785e-05
## GO:0032872 3/15 35/18888 2.611906e-06 1.247709e-03 5.077886e-04
## GO:0070302 3/15 38/18888 3.361733e-06 1.247709e-03 5.077886e-04
## GO:0070482 5/15 354/18888 5.784493e-06 1.247709e-03 5.077886e-04
## GO:0070665 4/15 164/18888 6.941399e-06 1.247709e-03 5.077886e-04
## GO:0051347 5/15 376/18888 7.756126e-06 1.247709e-03 5.077886e-04
## geneID Count
## GO:0051054 CDKN1A/MYC/AKT1/MAPK3/FOXM1/TFRC 6
## GO:0032872 MYC/MAPK3/FOXM1 3
## GO:0070302 MYC/MAPK3/FOXM1 3
## GO:0070482 CDKN1A/MYC/VHL/AKT1/TFRC 5
## GO:0070665 CDKN1A/MAPK3/TFRC/ANXA1 4
## GO:0051347 CDKN1A/MYC/AKT1/MAPK3/RET 5
## ID Description GeneRatio BgRatio
## GO:0005769 GO:0005769 early endosome 4/15 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane 3/15 255/19894
## GO:0016328 GO:0016328 lateral plasma membrane 2/15 68/19894
## GO:0009925 GO:0009925 basal plasma membrane 3/15 286/19894
## GO:0045178 GO:0045178 basal part of cell 3/15 305/19894
## GO:0070557 GO:0070557 PCNA-p21 complex 1/15 2/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005769 0.0002388682 0.01636673 0.01224104 MAPK3/RET/TFRC/ANXA1 4
## GO:0016323 0.0008449199 0.01636673 0.01224104 TFRC/CLDN7/ANXA1 3
## GO:0016328 0.0011745366 0.01636673 0.01224104 CLDN7/ANXA1 2
## GO:0009925 0.0011769074 0.01636673 0.01224104 TFRC/CLDN7/ANXA1 3
## GO:0045178 0.0014160699 0.01636673 0.01224104 TFRC/CLDN7/ANXA1 3
## GO:0070557 0.0015074617 0.01636673 0.01224104 CDKN1A 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")## Warning: ggrepel: 17 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")## Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")
#goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_glmnet_cox.rds")